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9qdp

De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2

Method: X-RAY DIFFRACTION D_max: 53.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdp
deposition_date	2025-03-06
title	De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2
keywords	Morita-Baylis-Hillman Enzyme, DE NOVO PROTEIN; DE NOVO PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	17.40 Å
rg_electron	16.06 Å
i0	8920970.00
molecular_weight	21764.0 kDa
excluded_volume	27161 Å³
envelope_volume	30739 Å³
shell_volume	15999 Å³
envelope_diameter	55.7 Å
shell_rg	22.17 Å
envelope_rg	16.15 Å
shape_rg	16.06 Å
total_rg	17.06 Å
total_atoms	3051
n_residues	206
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	53.5 Å
rg_real	17.24 Å
rg_real_error	0.29 Å
i0_real	8.9210e+06
i0_real_error	1.1130e+05
rg_reciprocal	17.26 Å
i0_reciprocal	8921000.0000
total_estimate	0.8953
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	-0.036
kurtosis	-0.548
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	1624000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2
formula_weight	23198.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3633

MGSSHHHHHHSSGENLYFQSGGEAARRAGEAFGEVLDAGDRANPALQPIADENRRFVRDHADLVERIYALAAEAIARLGTADPAAAAAVVAVMLGLLNVARLAAHLRDQGRDAEAEELLALAEEILRAALAGTPEEVTTTARAVGQAAWLAFVAGRSVELALENLRKVKEANLEERRAFAEEGEAASVRWLADTYGAEAAAAHLAAYAAGVAAAVAILQAS

Source

organism	Synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 2 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	420

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6. Citations (1)

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length_a	56.775 Å
length_b	51.881 Å
length_c	72.606 Å
angle_alpha	90.00 °
angle_beta	112.27 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.170 Å
resolution_low	36.750 Å
r_factor	0.1355
r_work	0.1340
r_free	0.1640

fit	/app/data/saxs_computation/qd/9qdp/9qdp.fit
pddf	/app/data/pr_computation/qd/9qdp/9qdp.pr.out
profile	/app/data/saxs_computation/qd/9qdp/9qdp.dat

De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction